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1 #!/usr/bin/env python
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2
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3 """
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4 Read a wiggle track and print out a series of lines containing
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5 "chrom position score". Ignores track lines, handles bed, variableStep
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6 and fixedStep wiggle lines.
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7 """
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8 import sys
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9 from galaxy import eggs
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10 import pkg_resources; pkg_resources.require( "bx-python" )
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11 import bx.wiggle
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12 from galaxy.tools.exception_handling import *
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13
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14 def stop_err( msg ):
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15 sys.stderr.write( msg )
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16 sys.exit()
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17
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18 def main():
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19 if len( sys.argv ) > 1:
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20 in_file = open( sys.argv[1] )
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21 else:
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22 in_file = open( sys.stdin )
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23
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24 if len( sys.argv ) > 2:
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25 out_file = open( sys.argv[2], "w" )
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26 else:
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27 out_file = sys.stdout
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28
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29 try:
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30 for fields in bx.wiggle.IntervalReader( UCSCOutWrapper( in_file ) ):
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31 out_file.write( "%s\n" % "\t".join( map( str, fields ) ) )
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32 except UCSCLimitException:
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33 # Wiggle data was truncated, at the very least need to warn the user.
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34 print 'Encountered message from UCSC: "Reached output limit of 100000 data values", so be aware your data was truncated.'
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35 except ValueError, e:
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36 in_file.close()
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37 out_file.close()
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38 stop_err( str( e ) )
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39
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40 in_file.close()
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41 out_file.close()
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42
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43 if __name__ == "__main__": main()
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